Endgame modifications have been a touchy subject for quite some time now due to a variety of reasons. To address some of these concerns, BioWare’s Senior Game Balance Designer Jason Attard took to the forums to speak on the subject.
Our goal is that a highly-skilled player can complete content without needing to swap mods on their gear, but spending the time and credits necessary to optimize the mods should still make a noticeable difference.
When we generate mods for endgame gear, we generate all the mod variants at a given item level and then run a process that combines the mods with endgame shell items to create the items needed for an Operation. This process helps us ensure that the stats are useful for Advanced Classes and roles, but it doesn't generate gear that is completely optimal for every spec. We always manually check the results and tweak items where necessary.
We have had some problems in the past with gear that stacks a single rating too much and with incorrect armorings being assigned to some items (high Endurance gear should go to tanking items, Aim/Cunning/Strength/Willpower should go into DPS and healing items), and we're continuing to refine the processes we use to make more useful gear. In future tiers, you'll see many issues with mod allocation corrected!
For the thread in full, head over to the official forum.